5KSD Transport Protein date Jul 08, 2016
title Crystal Structure Of A Plasma Membrane Proton Pump
authors T.Croll, B.P.Pedersen, P.Nissen
compound source
Molecule: Atpase 2, Plasma Membrane-Type
Chain: A, B
Synonym: Proton Pump 2
Ec: 3.6.3.6
Engineered: Yes
Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress
Organism_taxid: 3702
Gene: Aha2, At4g30190, F9n11.40
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Rs-72
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmp-652
symmetry Space Group: P 21 21 21
R_factor 0.287 R_Free 0.324
crystal
cell
length a length b length c angle alpha angle beta angle gamma
85.290 144.420 312.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand ACP, K, LMT, MG enzyme Hydrolase E.C.3.6.3.6 BRENDA
note 5KSD supersedes 3B8C
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the plasma membrane proton pump., Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Nissen P, Nature. 2007 Dec 13;450(7172):1111-4. PMID:18075595
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (577 Kb) [Save to disk]
  • Biological Unit Coordinates (5ksd.pdb1.gz) 287 Kb
  • Biological Unit Coordinates (5ksd.pdb2.gz) 287 Kb
  • LPC: Ligand-Protein Contacts for 5KSD
  • CSU: Contacts of Structural Units for 5KSD
  • Structure Factors (821 Kb)
  • Retrieve 5KSD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KSD from S2C, [Save to disk]
  • Re-refined 5ksd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KSD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5KSD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ksd_A] [5ksd] [5ksd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5KSD: [Cation_ATPase_N ] by SMART
  • Other resources with information on 5KSD
  • Community annotation for 5KSD at PDBWiki (http://pdbwiki.org)

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